Job ID = 4178399 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,364,174 reads read : 16,364,174 reads written : 16,364,174 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:44 16364174 reads; of these: 16364174 (100.00%) were unpaired; of these: 1051142 (6.42%) aligned 0 times 12998007 (79.43%) aligned exactly 1 time 2315025 (14.15%) aligned >1 times 93.58% overall alignment rate Time searching: 00:03:44 Overall time: 00:03:44 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1899509 / 15313032 = 0.1240 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:33:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107877/SRX4107877.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107877/SRX4107877.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107877/SRX4107877.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107877/SRX4107877.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 05 Dec 2019 12:33:10: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:33:10: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:33:18: 1000000 INFO @ Thu, 05 Dec 2019 12:33:27: 2000000 INFO @ Thu, 05 Dec 2019 12:33:35: 3000000 INFO @ Thu, 05 Dec 2019 12:33:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107877/SRX4107877.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107877/SRX4107877.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107877/SRX4107877.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107877/SRX4107877.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 05 Dec 2019 12:33:38: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:33:38: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:33:43: 4000000 INFO @ Thu, 05 Dec 2019 12:33:46: 1000000 INFO @ Thu, 05 Dec 2019 12:33:52: 5000000 INFO @ Thu, 05 Dec 2019 12:33:54: 2000000 INFO @ Thu, 05 Dec 2019 12:34:00: 6000000 INFO @ Thu, 05 Dec 2019 12:34:01: 3000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:34:08: 7000000 INFO @ Thu, 05 Dec 2019 12:34:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107877/SRX4107877.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107877/SRX4107877.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107877/SRX4107877.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107877/SRX4107877.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 05 Dec 2019 12:34:09: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:34:09: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:34:09: 4000000 INFO @ Thu, 05 Dec 2019 12:34:17: 5000000 INFO @ Thu, 05 Dec 2019 12:34:17: 8000000 INFO @ Thu, 05 Dec 2019 12:34:17: 1000000 INFO @ Thu, 05 Dec 2019 12:34:25: 9000000 INFO @ Thu, 05 Dec 2019 12:34:27: 6000000 INFO @ Thu, 05 Dec 2019 12:34:27: 2000000 INFO @ Thu, 05 Dec 2019 12:34:33: 10000000 INFO @ Thu, 05 Dec 2019 12:34:37: 7000000 INFO @ Thu, 05 Dec 2019 12:34:37: 3000000 INFO @ Thu, 05 Dec 2019 12:34:41: 11000000 INFO @ Thu, 05 Dec 2019 12:34:45: 4000000 INFO @ Thu, 05 Dec 2019 12:34:45: 8000000 INFO @ Thu, 05 Dec 2019 12:34:50: 12000000 INFO @ Thu, 05 Dec 2019 12:34:53: 5000000 INFO @ Thu, 05 Dec 2019 12:34:53: 9000000 INFO @ Thu, 05 Dec 2019 12:34:58: 13000000 INFO @ Thu, 05 Dec 2019 12:35:01: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:35:01: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:35:01: #1 total tags in treatment: 13413523 INFO @ Thu, 05 Dec 2019 12:35:01: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:35:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:35:01: 10000000 INFO @ Thu, 05 Dec 2019 12:35:01: #1 tags after filtering in treatment: 13413523 INFO @ Thu, 05 Dec 2019 12:35:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:35:01: #1 finished! INFO @ Thu, 05 Dec 2019 12:35:01: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:35:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:35:01: 6000000 INFO @ Thu, 05 Dec 2019 12:35:02: #2 number of paired peaks: 465 WARNING @ Thu, 05 Dec 2019 12:35:02: Fewer paired peaks (465) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 465 pairs to build model! INFO @ Thu, 05 Dec 2019 12:35:02: start model_add_line... INFO @ Thu, 05 Dec 2019 12:35:03: start X-correlation... INFO @ Thu, 05 Dec 2019 12:35:03: end of X-cor INFO @ Thu, 05 Dec 2019 12:35:03: #2 finished! INFO @ Thu, 05 Dec 2019 12:35:03: #2 predicted fragment length is 118 bps INFO @ Thu, 05 Dec 2019 12:35:03: #2 alternative fragment length(s) may be 118 bps INFO @ Thu, 05 Dec 2019 12:35:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107877/SRX4107877.05_model.r INFO @ Thu, 05 Dec 2019 12:35:03: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:35:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:35:11: 11000000 INFO @ Thu, 05 Dec 2019 12:35:12: 7000000 INFO @ Thu, 05 Dec 2019 12:35:21: 8000000 INFO @ Thu, 05 Dec 2019 12:35:21: 12000000 INFO @ Thu, 05 Dec 2019 12:35:28: 9000000 INFO @ Thu, 05 Dec 2019 12:35:30: 13000000 INFO @ Thu, 05 Dec 2019 12:35:33: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:35:33: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:35:33: #1 total tags in treatment: 13413523 INFO @ Thu, 05 Dec 2019 12:35:33: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:35:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:35:33: #1 tags after filtering in treatment: 13413523 INFO @ Thu, 05 Dec 2019 12:35:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:35:33: #1 finished! INFO @ Thu, 05 Dec 2019 12:35:33: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:35:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:35:34: #2 number of paired peaks: 465 WARNING @ Thu, 05 Dec 2019 12:35:34: Fewer paired peaks (465) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 465 pairs to build model! INFO @ Thu, 05 Dec 2019 12:35:34: start model_add_line... INFO @ Thu, 05 Dec 2019 12:35:35: start X-correlation... INFO @ Thu, 05 Dec 2019 12:35:35: end of X-cor INFO @ Thu, 05 Dec 2019 12:35:35: #2 finished! INFO @ Thu, 05 Dec 2019 12:35:35: #2 predicted fragment length is 118 bps INFO @ Thu, 05 Dec 2019 12:35:35: #2 alternative fragment length(s) may be 118 bps INFO @ Thu, 05 Dec 2019 12:35:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107877/SRX4107877.10_model.r INFO @ Thu, 05 Dec 2019 12:35:35: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:35:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:35:35: 10000000 INFO @ Thu, 05 Dec 2019 12:35:43: 11000000 INFO @ Thu, 05 Dec 2019 12:35:46: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:35:50: 12000000 INFO @ Thu, 05 Dec 2019 12:35:57: 13000000 INFO @ Thu, 05 Dec 2019 12:36:00: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:36:00: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:36:00: #1 total tags in treatment: 13413523 INFO @ Thu, 05 Dec 2019 12:36:00: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:36:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:36:00: #1 tags after filtering in treatment: 13413523 INFO @ Thu, 05 Dec 2019 12:36:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:36:00: #1 finished! INFO @ Thu, 05 Dec 2019 12:36:00: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:36:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:36:02: #2 number of paired peaks: 465 WARNING @ Thu, 05 Dec 2019 12:36:02: Fewer paired peaks (465) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 465 pairs to build model! INFO @ Thu, 05 Dec 2019 12:36:02: start model_add_line... INFO @ Thu, 05 Dec 2019 12:36:02: start X-correlation... INFO @ Thu, 05 Dec 2019 12:36:02: end of X-cor INFO @ Thu, 05 Dec 2019 12:36:02: #2 finished! INFO @ Thu, 05 Dec 2019 12:36:02: #2 predicted fragment length is 118 bps INFO @ Thu, 05 Dec 2019 12:36:02: #2 alternative fragment length(s) may be 118 bps INFO @ Thu, 05 Dec 2019 12:36:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107877/SRX4107877.20_model.r INFO @ Thu, 05 Dec 2019 12:36:02: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:36:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:36:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107877/SRX4107877.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:36:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107877/SRX4107877.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:36:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107877/SRX4107877.05_summits.bed INFO @ Thu, 05 Dec 2019 12:36:05: Done! pass1 - making usageList (7 chroms): 15 millis pass2 - checking and writing primary data (5013 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:36:12: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:36:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107877/SRX4107877.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:36:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107877/SRX4107877.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:36:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107877/SRX4107877.10_summits.bed INFO @ Thu, 05 Dec 2019 12:36:36: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3524 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:36:44: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:37:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107877/SRX4107877.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:37:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107877/SRX4107877.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:37:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107877/SRX4107877.20_summits.bed INFO @ Thu, 05 Dec 2019 12:37:03: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1972 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。